You have to totally reset the comment_count area in wordpress_posts '0' too - it stores it for the reason that table therefore it does not need to do the counts in the comments tables each time....

EDIT (according to comment):

You are able to run a simple query:

UPDATE wp_posts
set comment_count = 0

Be cautious :) this does not possess a where clause (a filter) so there's no returning when you do that. It is going to update all of your posts to achieve the comment count to become '0'. If you're able to create a backup of the DB, that might be good.

Also, is dependent on which tool you're using to operate the query, you may want to place the DB title: